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Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes

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Abstract

Despite the agricultural importance of both potato and tomato, very little is known about their chloroplast genomes. Analysis of the complete sequences of tomato, potato, tobacco, and Atropa chloroplast genomes reveals significant insertions and deletions within certain coding regions or regulatory sequences (e.g., deletion of repeated sequences within 16S rRNA, ycf2 or ribosomal binding sites in ycf2). RNA, photosynthesis, and atp synthase genes are the least divergent and the most divergent genes are clpP, cemA, ccsA, and matK. Repeat analyses identified 33–45 direct and inverted repeats ≥30 bp with a sequence identity of at least 90%; all but five of the repeats shared by all four Solanaceae genomes are located in the same genes or intergenic regions, suggesting a functional role. A comprehensive genome-wide analysis of all coding sequences and intergenic spacer regions was done for the first time in chloroplast genomes. Only four spacer regions are fully conserved (100% sequence identity) among all genomes; deletions or insertions within some intergenic spacer regions result in less than 25% sequence identity, underscoring the importance of choosing appropriate intergenic spacers for plastid transformation and providing valuable new information for phylogenetic utility of the chloroplast intergenic spacer regions. Comparison of coding sequences with expressed sequence tags showed considerable amount of variation, resulting in amino acid changes; none of the C-to-U conversions observed in potato and tomato were conserved in tobacco and Atropa. It is possible that there has been a loss of conserved editing sites in potato and tomato.

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Acknowledgments

Investigations reported in this article were supported in part by grants from USDA 3611-21000-017-00D to Henry Daniell and from NSF DEB 0120709 to Robert K. Jansen.

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  1. Department of Molecular Biology & Microbiology, Biomolecular Science, University of Central Florida, 4000 Central Florida Blvd, Bldg # 20, Room 336, Orlando, FL, 32816-2364, USA

    Henry Daniell, Seung-Bum Lee, Justin Grevich & Tania Quesada-Vargas

  2. Clemson University Genomics Institute, Biosystems Research Complex, Clemson University, 51 New Cherry Street, Clemson, SC, 29634, USA

    Christopher Saski & Jeffrey Tomkins

  3. Gen*NY*Sis Center for Excellence in Cancer Genomics, Department of Epidemiology & Biostatistics, University at Albany, State University of New York, 1 University Place, Rensselaer, NY, 12144, USA

    Chittibabu Guda

  4. Section of Integrative Biology and Institute of Cellular and Molecular Biology, Patterson Laboratories 141, University of Texas, Austin, TX, 78712, USA

    Robert K. Jansen

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  1. Henry Daniell
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Correspondence to Henry Daniell.

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Daniell, H., Lee, SB., Grevich, J. et al. Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor Appl Genet 112, 1503–1518 (2006). https://doi.org/10.1007/s00122-006-0254-x

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